7OD5: Reaction center protein H chain

F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LSP crystallization. Determined by X-ray diffraction at 2.1 Å resolution. Released 27 Apr 2022.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Rhodobacter sphaeroides
Chains: 3
Atoms: 7,703
Mol. weight: 100.71 kDa
Ligands: LDA, OLC, BCL, BPH
Released: 27 Apr 2022

Explore 7OD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OD5 contains 52 α-helices and 32 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	12-34	23
β-strand	43	1	1
β-strand	49	1	1
α-helix	50	1
α-helix	57-61	5
β-strand	62-66	5	2
β-strand	71-75	5	2
β-strand	87-89	3	3
β-strand	98-100	3	3
α-helix	104-107	4
α-helix	110-112	3
β-strand	123	1	4
β-strand	129	1	4
β-strand	131-133	3	5
α-helix	134-136	3
β-strand	141-144	4	5
α-helix	151	1
β-strand	152-154	3	5
β-strand	160-170	11	5
β-strand	175-183	9	5
β-strand	188-192	5	5
α-helix	193-195	3
β-strand	197-198	2	5
β-strand	203-204	2	5
α-helix	210-212	3
α-helix	217-219	3
α-helix	227-243	17
α-helix	245-247	3

Chain L: 18 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	7-9	3
β-strand	25-26	2	6
β-strand	29-30	2	6
α-helix	32-56	25
β-strand	65-66	2	7
α-helix	67-70	4
α-helix	71-73	3
α-helix	80-82	3
α-helix	84-111	28
α-helix	116-129	14
α-helix	130-134	5
α-helix	135-139	5
α-helix	142-144	3
α-helix	146-147	2
β-strand	148-149	2	7
α-helix	152-162	11
α-helix	167-169	3
α-helix	171-198	28
α-helix	209-220	12
α-helix	226-249	24
β-strand	251	1	8
β-strand	255	1	8
α-helix	259-262	4
α-helix	270-273	4

Chain M: 22 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	5
α-helix	26-28	3
β-strand	29	1	9
α-helix	30-32	3
β-strand	35	1	10
α-helix	37-40	4
β-strand	46	1	10
β-strand	51	1	9
α-helix	53-77	25
α-helix	82-88	7
β-strand	94	1	11
α-helix	95-98	4
α-helix	99-101	3
α-helix	109-111	3
α-helix	113-139	27
α-helix	145-158	14
α-helix	159-163	5
α-helix	164-168	5
α-helix	171-173	3
α-helix	175-176	2
β-strand	177	1	11
α-helix	179-192	14
α-helix	196-198	3
α-helix	200-225	26
α-helix	227-229	3
α-helix	234-239	6
α-helix	243-256	14
α-helix	264-285	22
β-strand	287	1	12
β-strand	291	1	12
α-helix	294-301	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Reaction center protein H chain	H	protein	241	Rhodobacter sphaeroides	Q3J170 (AlphaFold model)
Reaction center protein L chain	L	protein	281	Rhodobacter sphaeroides	Q3J1A5 (AlphaFold model)
Reaction center protein M chain	M	protein	303	Rhodobacter sphaeroides	Q3J1A6 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>7OD5_1 Reaction center protein H chain (chains H)
NFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPH
GRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGH
NKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGST
RLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKR
K

Sequence of entity 2 (L), FASTA

>7OD5_2 Reaction center protein L chain (chains L)
ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWN
PQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFA
FAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAITFF
FTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSA
VFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING

Sequence of entity 3 (M), FASTA

>7OD5_3 Reaction center protein M chain (chains M)
AEYQNIFTQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSL
FSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASF
FMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIF
SHLDWTNNFSLVHGNLHYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIAD
RGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQN
HGM

Ligands and cofactors

ID	Name	Formula	Copies
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	4
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	1
BCL	Bacteriochlorophyll a	C55 H74 Mg N4 O6	4
BPH	Bacteriopheophytin a	C55 H76 N4 O6	2
NKP	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate	C21 H41 O7 P	2
FE	FE (III) ion	Fe	1
U10	Ubiquinone-10	C59 H90 O4	1
SPN	Speroidenone	C41 H70 O2	1

Water and common crystallization additives (UNL, EDO) are not listed.

Primary citation

X-ray structure of the Rhodobacter sphaeroides reaction center with an M197 Phe→His substitution clarifies the properties of the mutant complex. Selikhanov, G., Fufina, T., Guenther, S. et al. IUCrJ (2022) 9:261-271. DOI 10.1107/S2052252521013178 · PubMed

Other PDB entries of the same protein (UniProt Q3J170 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P2C 2.04 Å, F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides…
4IN5 2.2 Å, (M)L214G mutant of the Rhodobacter sphaeroides Reaction Center
7MH3 2.3 Å, Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant;…
5LRI 2.4 Å, Photosynthetic reaction center mutant with GLUL212 replaced with trp (chain L, EL212W)
8C87 2.45 Å, Double mutant A(L172)C/L(L246)C structure of Photosynthetic Reaction Center From…
7MH4 2.48 Å, Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant;…
7PIL 2.5 Å, Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
8C3F 2.6 Å, Double mutant I(L177)H/F(M197)H structure of Photosynthetic Reaction Center From…
8C5X 2.6 Å, Double mutant A(L37)C/S(L99)C structure of Photosynthetic Reaction Center From…
8C7C 2.6 Å, Double mutant V(M84)C/A(L278)C structure of Photosynthetic Reaction Center From…
2WX5 2.63 Å, Hexa-coordination of a bacteriochlorophyll cofactor in the Rhodobacter sphaeroides…
4IN6 2.7 Å, (M)L214A mutant of the Rhodobacter sphaeroides Reaction Center

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